FLOSS {ribosomeProfilingQC} | R Documentation

## Fragment Length Organization Similarity Score (FLOSS)

### Description

The FLOSS will be calculated from a histogram of read lengths for footprints on a transcript or reading frame.

### Usage

    FLOSS(
      reads,
      ref,
      CDS,
      readLengths = c(26:34),
      level = c("tx", "gene"),
      draw = FALSE
    )

### Arguments

`reads` | Output of getPsiteCoordinates
`ref` | Refercence id list. If level is set to tx, the id should be transcript names. If level is set to gene, the id should be gene id.
`CDS` | Output of prepareCDS
`readLengths` | Read length used for calculation
`level` | Transcript or gene level
`draw` | Plot FLOSS vs total reads or not.

### Value

A data frame with colnames as id, FLOSS, totalReads, wilcox.test.pval, cook's distance.

### References

1: Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 2014 Sep 11;8(5):1365-79. doi: 10.1016/j.celrep.2014.07.045. Epub 2014 Aug 21. PubMed PMID: 25159147; PubMed Central PMCID: PMC4216110.

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    pc <- getPsiteCoordinates(bamfile, bestpsite=13)
    #library(GenomicFeatures)
    library(BSgenome.Drerio.UCSC.danRer10)
    #txdb <- makeTxDbFromGFF(system.file("extdata",
     #         "Danio_rerio.GRCz10.91.chr1.gtf.gz",
     #         package="ribosomeProfilingQC"),
     #         organism = "Danio rerio",
     #         chrominfo = seqinfo(Drerio)["chr1"],
     #         taxonomyId = 7955)
    #CDS <- prepareCDS(txdb)
    CDS <- readRDS(system.file("extdata", "CDS.rds",
                               package="ribosomeProfilingQC"))
    set.seed(123)
    ref <- sample(unique(CDS$gene_id), 100)
    fl <- FLOSS(pc, ref, CDS, level="gene")

[Package ribosomeProfilingQC version 0.99.9 Index]